A system and method for synchronizing messages between client application instances and a message service provider includes a connection service communicatively coupled to a plurality of client messaging application instances; a first intermediary transfer layer with an inbound message data queue that queues message updates of a client application instance and an outbound message data queue that queues message updates and notifications from a mailbox service layer; a mailbox service layer communicatively coupled to the connection service through the first intermediary transfer layer; a second intermediary transfer layer with an mailbox message data queue that contains queued message data directed at the mailbox service layer and a message service data queue that contains queued message updates directed at a message service layer; and a message service layer configured for message interactions with an outside message service provider.